Strandedness. reportBed in bedFile. peIntersect

	1. Added strandedness to relevant programs (e.g. intersectBed, mergeBed, etc.)
	2. Moved reportBed and reportBedRange to bedFile.cpp to clean up code
	3. Sped up file parsing.  Added lineFileUtilities.cpp
	4. Added peIntersectBed
Added version.h to simplify versioning
Added "inspan" and "outspan" to peIntersectBed
Updated USAGE_EXAMPLES to include peIntersectBed
Updated master Makefile and fixed bug in genomeCoverage

	1.  Changed master Makefile to compile utils first.
	2.  Fixed obvious bug in calculating discrete DOC in genomeCoverageBed
		--Identified by Scott Dewell, Rockefeller University.  Thanks!
Removed extraneous testing files.
BEDTools Public Release 2.0
Updated documents to say Version 2.0
Added UCSC browser header support.  Fixed bug in mergeBed.  Release 2.0.1
Updated VERSION and removed extraneous files.
Allowed empty lines in bedFile.cpp
Updated version.h to 2.0.1
Fixed bug in peIntersectBed when using stdin.

	1. When using stdin, the "inspan" annd "outspan" modes were not working.
	   Simple bug in the if statement...copy and paste error.
VERSION 2.1.0
	1. Fixed a bug in peIntersectBed that prevented -a from being correctly handled when passed via stdin.
	2. Added new functionality to coverageBed that calculates the density of coverage.
	3. Fixed bug in genomeCoverageBed.
Changed BED.score to int from ushort
Changed BEDPE.score to int from ushort
Version 2.1.1

	1. Added limits.h to bedFile.h to prevent compilation errors on some systems.
	2. Fixed the bedFile.cpp parsing logic to allow proper parsing of track and browser lines
Updated ancillary files for Version 2.1.1
Updated the help message for fastaFromBed
	- Added the -name parameter.  It was missing, so users had no idea it existed.
Changed the score field to be a string to allow greater BED flexibility.